BVH Export/Import, Armature different when re-imported
The BVH format stores bones differently to Blender.

Specifically, it doesn't support bone-length and bone-roll, each bone is just a joint(as if you have many parented empties in Blender), so this information is lost on export, when the BVH is imported back in, the animation will match the original, but not the armature.

The bone lengths &amp; roll have to be calculated on import (because its not in the file).

This is simply a limitation of the BVH format, or a difference at least, with Blender's armature representation.